SMN controls neuromuscular junction integrity through U7 snRNP

The neuromuscular junction (NMJ) is an essential synapse for animal survival whose loss is a key hallmark of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA). While insights into the function of the causative genes implicate RNA dysregulation in NMJ pathogenesis, the RNA-mediated mechanisms controlling the biology of this specialized synapse that go awry in disease remain elusive. Here, we show that activity of the SMA-determining SMN protein in the assembly of U7 small nuclear ribonucleoprotein (snRNP), which functions in the 3'-end processing of replication-dependent histone mRNAs, is required for NMJ integrity. AAV9-mediated gene delivery of U7-specific Lsm10 and Lsm11 proteins selectively enhances U7 snRNP assembly, corrects histone mRNA processing defects, and rescues key structural and functional abnormalities of neuromuscular pathology in SMA mice - including NMJ denervation, reduced synaptic transmission, and skeletal muscle atrophy. Furthermore, U7 snRNP dysfunction induced by SMN deficiency drives selective loss of the synaptic organizing protein Agrin at NMJs innervating vulnerable axial muscles of SMA mice, revealing an unanticipated link between U7-dependent histone mRNA processing and motor neuron-derived expression of an essential factor for NMJ biology. Together, these findings establish a direct contribution of U7 snRNP dysfunction to the neuromuscular phenotype in SMA and the requirement of RNA-mediated histone gene regulation for maintaining functional synaptic connections between motor neurons and muscles.

U7 deciphered: the mechanism that forms the unusual 3′ end of metazoan replication-dependent histone mRNAs

In animal cells, replication-dependent histone mRNAs end with a highly conserved stem–loop structure followed by a 4- to 5-nucleotide single-stranded tail. This unique 3′ end distinguishes replication-dependent histone mRNAs from all other eukaryotic mRNAs, which end with a poly(A) tail produced by the canonical 3′-end processing mechanism of cleavage and polyadenylation. The pioneering studies of Max Birnstiel's group demonstrated nearly 40 years ago that the unique 3′ end of animal replication-dependent histone mRNAs is generated by a distinct processing mechanism, whereby histone mRNA precursors are cleaved downstream of the stem–loop, but this cleavage is not followed by polyadenylation. The key role is played by the U7 snRNP, a complex of a ∼60 nucleotide U7 snRNA and many proteins. Some of these proteins, including the enzymatic component CPSF73, are shared with the canonical cleavage and polyadenylation machinery, justifying the view that the two metazoan pre-mRNA 3′-end processing mechanisms have a common evolutionary origin. The studies on U7 snRNP culminated in the recent breakthrough of reconstituting an entirely recombinant human machinery that is capable of accurately cleaving histone pre-mRNAs, and determining its structure in complex with a pre-mRNA substrate (with 13 proteins and two RNAs) that is poised for the cleavage reaction. The structure uncovered an unanticipated network of interactions within the U7 snRNP and a remarkable mechanism of activating catalytically dormant CPSF73 for the cleavage. This work provides a conceptual framework for understanding other eukaryotic 3′-end processing machineries.

Small nuclear ribonucleoproteins (snRNPs) based gene therapy

In 1968, Weinberg and Penman initially coined the term snRNA. Splicing is the process of eliminating introns from pre-RNA and combining exons The two forms of splicing are constitutive and alternative. U7 snRNP is a critical element in the unique 3′ end processing of replication-dependent histone (RDH) premRNAs. U7 Sm OPT uses antisense oligonucleotides to control pre-mRNA splicing. U7 snRNP has shown potential in preclinical studies and human clinical trials. DMD, ALS, thalassemia, HIV-1 infection, and spinal muscular atrophy are excellent illustrations of the majority of the problems (SMA) SmD1 and SmD2, which are found in other U snRNPs, are replaced by Lsm10 and Lsm11, respectively. There are just 500 molecules of U7SnRNP in a cell. Interesting because of its size, great stability, and tendency to collect in the nucleus of U 7 snRNA. The snRNP particle may hybridize to practically any RNA sequence in the nucleoplasm by altering the motif.U7 snRNA gene therapy is often employed to repair splicing abnormalities. The utilization of U7 Sm OPT-implanted antisense oligonucleotides has a multitude of potential therapeutic applications. More effective are the locations that bind U1 and U2 snRNPs to suppress splicing. useful for addressing splicing mistakes in muscular dystrophy, DMD, ALS, thalassemia, HIV-1 infection, and SMA PTCH1, BRCA1, and CYP11A have all been fixed with it. X-linked recessive muscular wasting illness, DMD. Individuals with exon 2 deletions either have asymptomatic or mildly symptomatic dystrophin levels. ANTISENSE oligonucleotides were introduced into the U7 Sm OPT and given via AAV to treat patients. These cells missed exon 2, resulting in an alternative translation starting at exon 6. (through an internal ribosome entrance region) The NIH's next clinical study will commence in January of 2020. U7 Sm OPT bifunctional gene therapy was successful in treating muscular dystrophy.Superoxide dismutase 1 (SOD1) gene mutations cause amyotrophic lateral sclerosis (ALS). SOD1 function was restored in a single study using U7Sm OPT to help rats with ALS. When given at birth, this medicine postponed sickness onset and enhanced life expectancy by 92% and 58%, respectively. Mutations in intron 2 produce a premature stop codon and hinder translation of full-length globin. Antisense oligonucleotides that span this region target nucleotides 102 to 130 of globin mRNA exon 1.5′ or 3′ splice site oligonucleotides in mammalian cells have been found to fix globin mRNA. The 654T > G mutation causes severe thalassemia symptoms. Combining U7 Sm OPT with induced pluripotent stem cells (iPSCs) led to a successful decrease of the globin gene

ALS-linked FUS mutants affect the localization of U7 snRNP and replication-dependent histone gene expression in human cells

Genes encoding replication-dependent histones lack introns, and the mRNAs produced are a unique class of RNA polymerase II transcripts in eukaryotic cells that do not end in a polyadenylated tail. Mature mRNAs are thus formed by a single endonucleolytic cleavage that releases the pre-mRNA from the DNA and is the only processing event necessary. U7 snRNP is one of the key factors that determines the cleavage site within the 3ʹUTR of replication-dependent histone pre-mRNAs. We have previously showed that the FUS protein interacts with U7 snRNA/snRNP and regulates the expression of histone genes by stimulating transcription and 3ʹ end maturation. Mutations in the FUS gene first identified in patients with amyotrophic lateral sclerosis (ALS) lead to the accumulation of the FUS protein in cytoplasmic inclusions. Here, we report that mutations in FUS lead to disruption of the transcriptional activity of FUS and mislocalization of U7 snRNA/snRNP in cytoplasmic aggregates in cellular models and primary neurons. As a consequence, decreased transcriptional efficiency and aberrant 3ʹ end processing of histone pre-mRNAs were observed. This study highlights for the first time the deregulation of replication-dependent histone gene expression and its involvement in ALS.

Composition and processing activity of a semi-recombinant holo U7 snRNP

In animal cells, replication-dependent histone pre-mRNAs are cleaved at the 3′ end by U7 snRNP consisting of two core components: a ∼60-nucleotide U7 snRNA and a ring of seven proteins, with Lsm10 and Lsm11 replacing the spliceosomal SmD1 and SmD2. Lsm11 interacts with FLASH and together they recruit the endonuclease CPSF73 and other polyadenylation factors, forming catalytically active holo U7 snRNP. Here, we assembled core U7 snRNP bound to FLASH from recombinant components and analyzed its appearance by electron microscopy and ability to support histone pre-mRNA processing in the presence of polyadenylation factors from nuclear extracts. We demonstrate that semi-recombinant holo U7 snRNP reconstituted in this manner has the same composition and functional properties as endogenous U7 snRNP, and accurately cleaves histone pre-mRNAs in a reconstituted in vitro processing reaction. We also demonstrate that the U7-specific Sm ring assembles efficiently in vitro on a spliceosomal Sm site but the engineered U7 snRNP is functionally impaired. This approach offers a unique opportunity to study the importance of various regions in the Sm proteins and U7 snRNA in 3′ end processing of histone pre-mRNAs.

Concentrating pre-mRNA processing factors in the histone locus body facilitates efficient histone mRNA biogenesis

The histone locus body (HLB) assembles at replication-dependent histone genes and concentrates factors required for histone messenger RNA (mRNA) biosynthesis. FLASH (Flice-associated huge protein) and U7 small nuclear RNP (snRNP) are HLB components that participate in 3′ processing of the nonpolyadenylated histone mRNAs by recruiting the endonuclease CPSF-73 to histone pre-mRNA. Using transgenes to complement a FLASH mutant, we show that distinct domains of FLASH involved in U7 snRNP binding, histone pre-mRNA cleavage, and HLB localization are all required for proper FLASH function in vivo. By genetically manipulating HLB composition using mutations in FLASH, mutations in the HLB assembly factor Mxc, or depletion of the variant histone H2aV, we find that failure to concentrate FLASH and/or U7 snRNP in the HLB impairs histone pre-mRNA processing. This failure results in accumulation of small amounts of polyadenylated histone mRNA and nascent read-through transcripts at the histone locus. Thus, the HLB concentrates FLASH and U7 snRNP, promoting efficient histone mRNA biosynthesis and coupling 3′ end processing with transcription termination.